Genome BLAST distance phylogenies inferred from whole plastid and whole mitochondrion genome sequences.

ABSTRACT:

Background

Phylogenetic methods which do not rely on multiple sequence alignments are important tools in inferring trees directly from completely sequenced genomes. Here, we extend the recently described Genome BLAST Distance Phylogeny (GBDP) strategy to compute phylogenetic trees from all completely sequenced plastid genomes currently available and from a selection of mitochondrial genomes representing the major eukaryotic lineages. BLASTN, TBLASTX, or combinations of both are used to locate high-scoring segment pairs (HSPs) between two sequences from which pairwise similarities and distances are computed in different ways resulting in a total of 96 GBDP variants. The suitability of these distance formulae for phylogeny reconstruction is directly estimated by computing a recently

SUBMITTER: Auch AF 

PROVIDER: S-EPMC1564419 | biostudies-literature | 2006 Jul

REPOSITORIES: biostudies-literature